Fusarium Basal Rot disease could decrease shallots harvest reaching more than 65%. This research’s aim was to study the resistance of several shallots varieties and the effect of the biological control agents application on Fusarium Basal Rot disease. This research was used a factorial Completely Randomized Design (CRD) with two factors. The first factor was shallot varieties (Bima, Tajuk, Bauji and Super Philip). The second factor was biological control agents (without biological control agents, Trichoderma, Gliocladium, Mycorrhiza, and a combination of Trichoderma and Gliocladium). The research data were analyzed with Analysis of Variance (ANOVA) at α= 5% level. If there was a significant difference, it was further tested using Duncan’s Multiple Range Test (DMRT) at α= 5% level. The results showed that regarding the resistance level to Fusarium Basal Rot disease was varied. They were resistant (Bima variety), moderately resistant (Bauji variety), and moderately susceptible (Super Philip and Tajuk varieties). Trichoderma was more effective in controlling Fusarium Basal Rot disease than the combination with Gliocladium. The application of Gliocladium was effective in controlling Fusarium Basal Rot disease on Tajuk and Super Philip varieties. The application of Mycorrhiza was not effective in controlling Fusarium Basal Rot disease.